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MySQL configuration for OrthoMCL

Overview

OrthoMCL is a program that aids in the identification of orthologs.  The OrthoMCL tool uses NCBI BLAST and the MCL application in conjunction with a relational database (MySQL).  OrthoMCL version 2.0.2 is available on the HPCC and can be loaded as a module.

However, because of the relational database requirement, the HPCC must be contacted in advance to setup a database for your runs. This tutorial briefly describes how to obtain access to the program, and how to use configuration files provided by the HPCC.

Database Access

Before beginning your HPCC runs, you will need to complete an help request ticket request to request a database and MySQL account for your use of OrthoMCL.   This information will be provided to you in the form of a configuration file, and you save this to your directory.  You can use the filename as a command-line argument to relevant scripts comprising the OrthoMCL application, which tell OrthMCL how to connect to your database. 

Configuration File

The following is an example of the configuration file you will receive:

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dbVendor=mysql
dbConnectString=dbi:mysql:someUserdb:db-01:3306
dbLogin=someUser
dbPassword=somePassword
# DO NOT CHANGE ANYTHING ABOVE THIS LINE UNLESS YOU KNOW WHAT YOU'RE DOING
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5

Command Example

A typical run that would require the database configuration file might look something like the following:

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orthomclPairs orthomcl.config log_file cleanup=[yes|no|only|all] <startAfter=TAG>

In the example above, the file "orthomcl.config" is the name of the configuration/connection file (provided by the HPCC) that you want to use for your run.

Purging the Database Between Runs

To facilitate multiple concurrent, or faster consecutive runs, many users ask for more than one database at setup time.  HPCC will typically be able to provide you with up to four (4) such databases.  Please specify this in your request.

Once your run is completed, you will need to purge the database of its contents prior to beginning new runs using the same database.  To have this performed, please contact ICER  via https://contact.icer.msu.edu, select "other" in the form and let us know you need your database purge and the name of the database  if you have multiple databases (or just provide the connection string like dbConnectString=dbi:mysql:someUserdb:db-01:3306 ).

When your work with OrthoMCL is complete, please notify the staff via the ICER contact form so we can purge your databases from the system.

Modifying the Configuration File

Most users will not need to modify the configuration file provided by the HPCC.  The most common modification needed will be to change the name of the database to be accessed in those cases where users are provided with access to more than one database.

The relevant line to be modified is shown below:

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dbConnectString=dbi:mysql:someUserdb:db-01:3306

In the example above, the database name is "someUserdb".  

Let's assume (for example), a user had been issued 4 databases named: someUserdb, someUserdb2, someUserdb3, someUserdb4.  To perform a run using one of these other databases, we would need to make a copy of the configuration file and change the name in that file, for example:

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dbConnectString=dbi:mysql:someUserdb2:db-01:3306

You may then structure the command for each OrthoMCL run to use the configuration file (and related database) desired.

More Information

Refer to the OrthoMCL User Manual.